GTF2E2 p.Ser71=
c.213T>C · rs987931337 · VCV1628220
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 3 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 12.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
Admixed American · 12/59,892 alleles
Filtering AF
0.0115%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.009%
Overall
0.00118%
19/1,609,358 alleles · ultra-rare
exomes 7/1,457,146 · genomes 12/152,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.02% | 4,991 |
| Remaining individualsnot grpmax-eligible | 0.00964% | 10,378 |
| African / African-American | 0.00134% | 74,804 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- GTF2E2
- Protein
- p.Ser71=
- Coding
- c.213T>C
- MANE Select
- NM_002095
- dbSNP
- rs987931337
- Type
- single nucleotide variant
- Location
- chr8:30635077 (GRCh38)
- Gene constraint
- LOEUF 1.107 · pLI 0.40 (gnomAD)
- Structure
- AlphaFold pLDDT 68.97 · 46 PDB
- Residue 71
- a DNA-binding region
Similar variants
- GTF2E2 p.Ala138Thr Uncertain significance ★★ ⚠ same type
- GTF2E2 p.Ala278Ser Uncertain significance ★★ ⚠ same type
- GTF2E2 p.Arg25Cys Uncertain significance ★★ ⚠ same type
- GTF2E2 p.Arg269Cys Uncertain significance ★★ ⚠ same type
- GTF2E2 p.Gly47Ala Uncertain significance ★★ ⚠ same type
- GTF2E2 p.His158Arg Uncertain significance ★★ ⚠ same type
- GTF2E2 p.Lys197Arg Uncertain significance ★★ ⚠ same type
- GTF2E2 p.Phe62Ile Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/gtf2e2-p-ser71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown